ArticleBMC systems biology2014
Quartet-based methods to reconstruct phylogenetic networks.
Article in BMC systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes.Journal of mathematical biology · 2021Article
- Evaluation of the MGISEQ-2000 Sequencing Platform for Illumina Target Capture Sequencing Libraries.Frontiers in genetics · 2021Article
- Artificial Intelligence Systems for Diagnosis and Clinical Classification of COVID-19.Frontiers in microbiology · 2021Article
- Clustering and classification methods for single-cell RNA-sequencing data.Briefings in bioinformatics · 2020Review
- Identification of Phage Viral Proteins With Hybrid Sequence Features.Frontiers in microbiology · 2019Article
- A Random Forest Sub-Golgi Protein Classifier Optimized via Dipeptide and Amino Acid Composition Features.Frontiers in bioengineering and biotechnology · 2019Article
- Genetic Polymorphism Study onBioMed research international · 2018Article
- De Novo Sequencing of aThe Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2018Article
- Pathogenicity and Whole Genome Sequence Analysis of a Pseudorabies Virus Strain FJ-2012 Isolated from Fujian, Southern China.The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2017Article
- Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting.PLoS genetics · 2016Article
- Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers.Evolutionary bioinformatics online · 2015Article
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4 authors.
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Abstract
backgroundPhylogenetic networks are employed to visualize evolutionary relationships among a group of nucleotide sequences, genes or species when reticulate events like hybridization, recombination, reassortant and horizontal gene transfer are believed to be involved. In comparison to traditional distance-based methods, quartet-based methods consider more information in the reconstruction process and thus have the potential to be more accurate.
resultsWe introduce QuartetSuite, which includes a set of new quartet-based methods, namely QuartetS, QuartetA, and QuartetM, to reconstruct phylogenetic networks from nucleotide sequences. We tested their performances and compared them with other popular methods on two simulated nucleotide sequence data sets: one generated from a tree topology and the other from a complicated evolutionary history containing three reticulate events. We further validated these methods to two real data sets: a bacterial data set consisting of seven concatenated genes of 36 bacterial species and an influenza data set related to recently emerging H7N9 low pathogenic avian influenza viruses in China.
conclusionQuartetS, QuartetA, and QuartetM have the potential to accurately reconstruct evolutionary scenarios from simple branching trees to complicated networks containing many reticulate events. These methods could provide insights into the understanding of complicated biological evolutionary processes such as bacterial taxonomy and reassortant of influenza viruses.
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